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Major threat that Pakistan faces today is water scarcity and any significant change in water availability from storage reservoirs coupled with below normal precipitation threatens food security of more than 207 million people. Two major reservoirs of Tarbela and Mangla on Indus and Jhelum rivers are studied. Landsat satellite’s data are used to estimate the water extents of these reservoirs during 1981–2017. A long-term significant decrease of 15–25% decade−1 in water extent is found for Tarbela as compared to 37–70% decade−1 for Mangla, mainly during March to June. Significant water extents reductions are observed in the range of −23.9 to −53.4 km2 (1991–2017) and −63.1 to −52.3 km2 (2001–2010 and 2011–2017) for Tarbela and Mangla, respectively. The precipitation amount and areas receiving this precipitation show a significant decreasing trend of −4.68 to −8.40 mm year−1 and −358.1 to −309.9 km2 year−1 for basins of Mangla and Tarbela, respectively. The precipitation and climatic oscillations are playing roles in variability of water extents. The ensuing multiple linear regression models predict water extents with an average error of 13% and 16% for Tarbela and Mangla, respectively.